#!/bin/bash -e

function info() {
    echo Usage: `basename $0` [-p out_prefix -s out_suffix] vcf
    exit 1
}

while getopts ":p:s:t:" opt; do
    case $opt in
        p) out_prefix=$OPTARG;;
        s) out_suffix=$OPTARG;;
        t) threads=$OPTARG;;
        ?) info;;
    esac
done
shift $(($OPTIND - 1))

if [ $# -lt 1 ]; then info; fi

. $var || :

$java_run/picard0 MakeSitesOnlyVcf \
    I=$1 \
    O=$out_prefix.site_only.vcf.gz

. $cmd_done

